The arrival of the Boraal would be the introduction of a foreign life form into an ecosystem not equipped to deal with it.

Please remember Vanyel, the Federation engages in interstellar colonization, Humans (just as a example) are on dozens of worlds. Moving the Boraal isn't a one of a kind experiment, they know how to do this because moving a intelligent species from one world to another is something they have considerable experience in.

If their arrival meant the destruction of the new planet's ecosystem, they would die. No ecosystem, no life, no chance.

True, that unlikely hypothetical could happen. But again, if they stay where they started, they definitely die out as a species, all that they are would be gone.

It's the difference between a statistical probability, and a absolute certainty.